Contacts of the helix formed by residues 708 - 713 (chain J) in PDB entry 1SOJ


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLY 708 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    704J  PHE      3.4     4.4    +      -       -      -
    705J  GLN*     3.3    13.0    +      -       -      -
    707J  THR*     1.3    79.3    +      -       -      +
    709J  LEU*     1.3    64.9    +      -       -      +
    710J  LEU*     3.1     3.4    -      -       -      -
    711J  GLU*     2.9    20.4    +      -       -      +
    712J  ILE*     2.9    21.1    +      -       -      +
    790J  LYS*     4.6     9.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 709 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    704J  PHE*     3.3    29.2    +      -       +      +
    707J  THR*     3.3    18.9    +      -       -      +
    708J  GLY*     1.3    77.3    -      -       -      +
    710J  LEU*     1.3    63.0    +      -       -      +
    712J  ILE*     4.3     3.4    -      -       +      -
    713J  PHE*     3.2    49.8    +      -       +      -
    715J  ILE*     3.8     6.4    -      -       -      +
    787J  ILE*     3.4    25.8    -      -       +      -
    808J  ALA*     4.0     4.5    -      -       +      +
    812J  MET*     3.8    25.6    -      -       +      +
    815J  TYR*     3.8    30.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 710 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    701J  TYR*     3.9    23.1    -      -       +      +
    704J  PHE*     3.2    32.3    +      -       +      +
    705J  GLN*     3.5    34.3    -      -       +      +
    708J  GLY*     3.1     1.4    +      -       -      -
    709J  LEU*     1.3    77.5    -      -       -      +
    711J  GLU*     1.3    58.3    +      -       +      +
    714J  LYS*     3.1     5.9    +      -       -      -
    715J  ILE*     2.8    66.3    +      -       +      +
    716J  PRO      5.7     0.2    -      -       -      -
    717J  THR*     5.3     4.0    -      -       -      +
    720J  PHE*     4.5    11.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 711 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708J  GLY*     2.9    12.1    +      -       -      +
    710J  LEU*     1.3    79.9    -      -       +      +
    712J  ILE*     1.3    66.9    +      -       +      +
    713J  PHE      3.2     0.2    -      -       -      -
    714J  LYS*     3.0    59.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 712 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707J  THR      4.8     0.9    -      -       -      +
    708J  GLY*     2.9    21.9    +      -       -      +
    709J  LEU*     4.0     1.1    -      -       -      +
    711J  GLU*     1.3    78.3    -      -       +      +
    713J  PHE*     1.3    91.8    +      -       +      +
    714J  LYS*     3.7     0.5    +      -       -      -
    779J  ILE*     3.9    18.2    -      -       -      +
    785J  ALA*     3.7    23.1    -      -       +      -
    786J  TYR      4.2    13.0    -      -       -      +
    787J  ILE*     3.6    31.6    -      -       +      -
    808J  ALA*     4.0     8.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 713 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    709J  LEU*     3.2    36.6    +      -       +      -
    712J  ILE*     1.3    99.0    -      -       +      +
    714J  LYS*     1.3    74.0    +      -       -      +
    715J  ILE*     3.1    18.4    +      -       +      +
    779J  ILE*     4.0     8.5    -      -       +      -
    785J  ALA*     5.4     2.0    -      -       +      -
    808J  ALA*     4.1     4.0    -      -       +      -
    809J  LEU*     3.8    46.4    -      -       +      -
    812J  MET*     3.7    18.4    -      -       +      -
    870J  PHE      5.2     1.0    -      -       -      +
    871J  LEU*     6.1     0.5    -      -       -      -
    873J  HIS*     3.7    14.1    +      -       -      +
    874J  LEU*     3.2    30.5    -      -       +      +
    878J  GLU*     5.4     7.6    -      -       -      -
----------------------------------------------------------
 Back to top of page


A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il